Generation of Potato Genome Sequence and Annotation Resources

The potato (Solanum tuberosum L.) is the fourth most important crop in the world, behind wheat, rice, and maize. In 2004, worldwide production of potatoes exceeded 327 million metric tons. The potato produces more food energy and food value per unit of land area than any other crop. Compared to grain crops, the potato is a superior source of nutrition. However, among the major crop plants, the potato is arguably the most intensively managed. In addition, tuber quality requirements are complex and must be maintained during harvest and storage.

To improve our understanding of potato, we are participating in the International Potato Genome Sequencing Consortium (PGSC). The PGSC has sequenced two potato species: the heterozygous diploid S. tuberosum Group Tuberosum cultivar, RH89-039-16 (RH), and the doubled monoploid S. tuberosum Group Phureja clone DM1-3 516R44 (DM). The DM genome has been assembled, annotated and released. You can access the genome through this site and/or through the Potato Genome Sequencing Consortium. The current potato genome assembly represents 726 Mb of which 86% is anchored to the genetic map. A total of 39,031 genes have been annotated in the DM genome. To aid in the annotation of the potato genome, we initiated a comprehensive whole transcriptome sequencing project for the DM clone in which 32 libraries were sequenced using RNA-seq. The RH genome has also been sequenced and next generation sequencing reads have been mapped to the DM genome assembly. Reads for the RH genome are available through EBI.

Participants:

• Principal Investigator (PI): C. Robin Buell, Michigan State University
• Co-Principal Investigator (coPI): Chris Town, J. Craig Venter Institute
• Collaborator: Jiming Jiang, University of Wisconsin-Madison
• Collaborator: Christine Flanagan, U. S. Botanic Garden

This project was initiated at TIGR on October 1, 2006, and as of October 1, 2007 moved to Michigan State University.

This material is based upon work supported by the National Science Foundation under Grant No. DBI-0604907 and DBI-0834044. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).